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  • genomes
  • In other organisms that do not show high growing rates or that present small genomes, codon usage optimization is normally absent, and codon preferences are determined by the characteristic mutational biases seen in that particular genome. (wikipedia.org)
  • gene expression
  • Different factors have been proposed to be related to codon usage bias, including gene expression level (reflecting selection for optimizing translation process by tRNA abundance), %G+C composition (reflecting horizontal gene transfer or mutational bias), GC skew (reflecting strand-specific mutational bias), amino acid conservation, protein hydropathy, transcriptional selection, RNA stability, optimal growth temperature, hypersaline adaptation and dietary nitrogen. (wikipedia.org)
  • rare codons
  • Although it has been shown that the rate of amino acid incorporation at more frequent codons occurs at a much higher rate than that of rare codons, the speed of translation has not been shown to be directly affected and therefore the bias towards more frequent codons may not be directly advantageous. (wikipedia.org)
  • In other words, some codons can undergo more changes and therefore result in lower equilibrium frequencies, also known as "rare" codons. (wikipedia.org)
  • Escherichia
  • Optimal codons in fast-growing microorganisms, like Escherichia coli or Saccharomyces cerevisiae (baker's yeast), reflect the composition of their respective genomic tRNA pool. (wikipedia.org)
  • tRNAs
  • At least one mathematical model has been developed where both codon usage and tRNA expression co-evolve in feedback fashion (i.e., codons already present in high frequencies drive up the expression of their corresponding tRNAs, and tRNAs normally expressed at high levels drive up the frequency of their corresponding codons). (wikipedia.org)
  • biases
  • It is generally acknowledged that codon biases reflect a balance between mutational biases and natural selection for translational optimization. (wikipedia.org)
  • The suggestion has been made that these codon biases play a role in the temporal regulation of their late proteins. (wikipedia.org)
  • proteins
  • Several viral families (herpesvirus, lentivirus, papillomavirus, polyomavirus, adenovirus, and parvovirus) are known to encode structural proteins that display heavily skewed codon usage compared to the host cell. (wikipedia.org)